alignment.yml

name: alignment
on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@v2

    - name: Free disk space (Ubuntu)
      uses: jlumbroso/free-disk-space@main
      with:
        tool-cache: false
        android: true
        dotnet: true
        haskell: true
        large-packages: true
        docker-images: true
        swap-storage: true

    - name: Set up Miniconda
      uses: conda-incubator/setup-miniconda@v2
      with:
        miniconda-version: "latest"
        activate-environment: test-env
        python-version: "3.10"

    - name: Install dependencies
      shell: bash -l {0}
      run: |
        # Remove tmp files
        sudo rm -rf /tmp/*

        # Install conda packages
        conda env list
        conda info
        conda config --add channels defaults
        conda config --add channels bioconda
        conda config --add channels conda-forge
        conda config --set channel_priority strict
        conda install pandas
        conda install nextflow==23.10.0
        conda install pylint
        conda install coveralls
        conda install pytest
        conda install pytest-cov
                
        # Install nexus
        pip install . --verbose

    - name: Run linter
      shell: bash -l {0}
      run: |
        chmod +x lint.sh
        bash lint.sh

    - name: Run unit tests
      shell: bash -l {0}
      run: |
        chmod +x scripts/unittests/unittest_alignment.sh
        bash scripts/unittests/unittest_alignment.sh